Conowingo was originally located on the eastern bank of the Susquehanna River at the confluence of the Conowingo Creek with the river. Conowingo was at the rapids that were the first navigation obstacle on the Susquehanna upstream of the Chesapeake Bay, the location of an early stretch of canal. It was also the site of the Conowingo Bridge.

A 90 foot fall of the river at the rapids dictated the location of the Conowingo Dam and thus the resulting inundation of the Old Conowingo site by the subsequent Conowingo Reservoir. At the completion of the dam in 1928, the Conowingo Post Office was relocated to the hill above the dam.

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A new town, named Conowingo Village, was created in 1928, on the Harford County side of the dam. It was initially a company town to house the dam's plant managers and workers. From the 1980s to 2000, the power company leased the homes to non-workers. In October, 2000, the village was shuttered. And in 2001 the power company donated the land to the Maryland Department of Natural Resources and the buildings to the local fire companies for training.